library(ggplot2)
library(cowplot)
library(dplyr)##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(colorBlindness)
library(scales)
library(bestNormalize)
library(Rmisc)## Loading required package: lattice
## Loading required package: plyr
## ------------------------------------------------------------------------------
## You have loaded plyr after dplyr - this is likely to cause problems.
## If you need functions from both plyr and dplyr, please load plyr first, then dplyr:
## library(plyr); library(dplyr)
## ------------------------------------------------------------------------------
##
## Attaching package: 'plyr'
## The following objects are masked from 'package:dplyr':
##
## arrange, count, desc, failwith, id, mutate, rename, summarise,
## summarize
library(ggpubr)##
## Attaching package: 'ggpubr'
## The following object is masked from 'package:plyr':
##
## mutate
## The following object is masked from 'package:cowplot':
##
## get_legend
#home comp
#sub.tah <- read.csv('/Volumes/Macintosh HD/Users/nicolakriefall/Google Drive (nicfall@bu.edu)/Moorea_revisions/env_revised/substrate.csv',header=TRUE)
#work comp
sub.tah <- read.csv('~/nicfall@bu.edu - Google Drive/My Drive/Moorea_revisions/env_revised/substrate.csv',header=TRUE)
sub <- subset(sub.tah,Marine.Area!="Tahiti Faaa")
sub$Substrate <- as.factor(sub$Substrate)
#str(sub)
##total proportion
sub$prop.test <- (sub$proportion)/3
##rename sites & habitats
sub$Marine.Area <- as.factor(sub$Marine.Area)
levels(sub$Marine.Area)## [1] "Maatea" "Tiahura"
levels(sub$Marine.Area) <- c("Mo'orea SE","Mo'orea NW")
levels(sub$Marine.Area)## [1] "Mo'orea SE" "Mo'orea NW"
sub$Marine.Area <- factor(sub$Marine.Area, levels=c("Mo'orea NW","Mo'orea SE")) #reorder
sub$Habitat <- as.factor(sub$Habitat)
levels(sub$Habitat)## [1] "Barrier reef" "Outer slope"
levels(sub$Habitat) <- c("Back","Fore")
levels(sub$Habitat)## [1] "Back" "Fore"
##only interested in 2013 - year of collection
sub13 <- subset(sub,Year=="2013")
sub14 <- subset(sub,Year=="2014")ggplot(data=sub13, aes(x=Habitat, y=prop.test, fill=Substrate)) +
geom_bar(stat="identity")+
facet_wrap(~Marine.Area)+
theme_cowplot()+
ylab('Relative proportion')+
xlab('Reef zone')ggplot(data=sub14, aes(x=Habitat, y=prop.test, fill=Substrate)) +
geom_bar(stat="identity")+
facet_wrap(~Marine.Area)+
theme_cowplot()+
ylab('Relative proportion')+
xlab('Reef zone')#ggsave("substrate.png")sub13$Substrate <- gsub(" ","_",sub13$Substrate)
sub13$sub_cats <- recode(sub13$Substrate, Acropora="Coral", Asparagopsis="Algae", Cyanophyceae="Algae", Dead_coral="Abiotic substrata", Dictyota="Algae", Halimeda="Algae", Macroalgae="Algae", Millepora="Coral", Montastrea="Coral", Montipora="Coral", Napopora="Coral", Pavement="Abiotic substrata", Pavona="Coral", Pocillopora="Coral", Porites="Coral", Psammocora="Coral", Rubble="Abiotic substrata", Sand="Abiotic substrata", Stegastes_Turf="Algae", Synarea="Coral", Turbinaria="Coral")
pal <- hcl.colors(12,"Tofino")
show_col(pal)colorz <- c("#3B415E","#8FC67C","#818CC0")
sub3 <- ggplot(data=sub13, aes(x=Habitat, y=prop.test, fill=sub_cats)) +
geom_bar(stat="identity")+
facet_wrap(~Marine.Area)+ #just need to remove 'nrow' here to go back to grid
theme_cowplot()+
ylab('Relative proportion')+
xlab('Reef zone')+
scale_fill_manual(values=colorz,name="Substrate",labels=c("Abiotic","Algae","Coral"))
sub3#cvdPlot(sub3)
#ggsave("substrate_3cats.png",height=3.5) #can also go back to default if square
sub14$Substrate <- gsub(" ","_",sub14$Substrate)
sub14$sub_cats <- recode(sub14$Substrate, Acropora="Coral", Asparagopsis="Algae", Cyanophyceae="Algae", Dead_coral="Abiotic substrata", Dictyota="Algae", Halimeda="Algae", Macroalgae="Algae", Millepora="Coral", Montastrea="Coral", Montipora="Coral", Napopora="Coral", Pavement="Abiotic substrata", Pavona="Coral", Pocillopora="Coral", Porites="Coral", Psammocora="Coral", Rubble="Abiotic substrata", Sand="Abiotic substrata", Stegastes_Turf="Algae", Synarea="Coral", Turbinaria="Coral")
pal <- hcl.colors(12,"Tofino")
show_col(pal)colorz <- c("#3B415E","#8FC67C","#818CC0")
sub4 <- ggplot(data=sub14, aes(x=Habitat, y=prop.test, fill=sub_cats)) +
geom_bar(stat="identity")+
facet_wrap(~Marine.Area)+ #just need to remove 'nrow' here to go back to grid
theme_cowplot()+
ylab('Relative proportion')+
xlab('Reef zone')+
scale_fill_manual(values=colorz,name="Substrate",labels=c("Abiotic","Algae","Coral"))
sub4sub13$sub_cats_med <- recode(sub13$Substrate, Acropora="Coral - Acropora", Asparagopsis="Algae - Asparagopsis", Cyanophyceae="Algae - Cyanophyceae", Dead_coral="Abiotic (e.g. rubble, sand)", Dictyota="Algae - Dictyota", Halimeda="Algae - Halimeda", Macroalgae="Algae - Macroalgae", Millepora="Coral - Millepora", Montastrea="Coral - Montastrea", Montipora="Coral - Montipora", Napopora="Coral - Napopora", Pavement="Abiotic (e.g. rubble, sand)", Pavona="Coral - Pavona", Pocillopora="Coral - Pocillopora", Porites="Coral - Porites", Psammocora="Coral - Psammocora", Rubble="Abiotic (e.g. rubble, sand)", Sand="Abiotic (e.g. rubble, sand)", Stegastes_Turf="Algae - Stegastes Turf", Synarea="Coral - Synarea", Turbinaria="Coral - Turbinaria")
#greens for algae
#pal.gr <- hcl.colors(5,"Greens")
#show_col(pal.gr)
#pal.gr
#"#004616" "#30893B" "#81C07A" "#CAE8C1" "#F6FBF4"
#pal.bl <- hcl.colors(9,"BuPu")
#show_col(pal.bl)
#pal.bl
#"#540046" "#6E2072" "#8346A1" "#8674B8" "#9099CA" "#A3BAD9" "#BED6E6" "#DBECF3" "#F2FBFC"
colorz2 <- c("grey","#004616","#30893B","#81C07A","#CAE8C1","#F6FBF4","#540046","#6E2072","#8346A1","#8674B8","#9099CA","#A3BAD9","#BED6E6","#DBECF3","#F2FBFC")
sub.med <- ggplot(data=sub13, aes(x=Habitat, y=prop.test, fill=sub_cats_med)) +
geom_bar(stat="identity")+
facet_wrap(~Marine.Area)+ #just need to remove 'nrow' here to go back to grid
theme_cowplot()+
ylab('Relative proportion')+
xlab('Reef zone')+
scale_fill_manual(values=colorz2,name="Substrate")
sub.med#ggsave("substrate_medcats.png",height=4) #can also go back to default if square
#cvdPlot(sub.med)
sub14$sub_cats_med <- recode(sub14$Substrate, Acropora="Coral - Acropora", Asparagopsis="Algae - Asparagopsis", Cyanophyceae="Algae - Cyanophyceae", Dead_coral="Abiotic (e.g. rubble, sand)", Dictyota="Algae - Dictyota", Halimeda="Algae - Halimeda", Macroalgae="Algae - Macroalgae", Millepora="Coral - Millepora", Montastrea="Coral - Montastrea", Montipora="Coral - Montipora", Napopora="Coral - Napopora", Pavement="Abiotic (e.g. rubble, sand)", Pavona="Coral - Pavona", Pocillopora="Coral - Pocillopora", Porites="Coral - Porites", Psammocora="Coral - Psammocora", Rubble="Abiotic (e.g. rubble, sand)", Sand="Abiotic (e.g. rubble, sand)", Stegastes_Turf="Algae - Stegastes Turf", Synarea="Coral - Synarea", Turbinaria="Coral - Turbinaria")
#greens for algae
pal.gr <- hcl.colors(5,"Greens")
show_col(pal.gr)pal.gr## [1] "#004616" "#30893B" "#81C07A" "#CAE8C1" "#F6FBF4"
#"#004616" "#30893B" "#81C07A" "#CAE8C1" "#F6FBF4"
pal.bl <- hcl.colors(9,"BuPu")
show_col(pal.bl)pal.bl## [1] "#540046" "#6E2072" "#8346A1" "#8674B8" "#9099CA" "#A3BAD9" "#BED6E6"
## [8] "#DBECF3" "#F2FBFC"
#"#540046" "#6E2072" "#8346A1" "#8674B8" "#9099CA" "#A3BAD9" "#BED6E6" "#DBECF3" "#F2FBFC"
colorz2 <- c("grey","#004616","#30893B","#81C07A","#CAE8C1","#F6FBF4","#540046","#6E2072","#8346A1","#8674B8","#9099CA","#A3BAD9","#BED6E6","#DBECF3","#F2FBFC")
sub.med2 <- ggplot(data=sub14, aes(x=Habitat, y=prop.test, fill=sub_cats_med)) +
geom_bar(stat="identity")+
facet_wrap(~Marine.Area)+ #just need to remove 'nrow' here to go back to grid
theme_cowplot()+
ylab('Relative proportion')+
xlab('Reef zone')+
scale_fill_manual(values=colorz2,name="Substrate")
sub.med2#ggsave("substrate_medcats.png",height=4) #can also go back to default if square
#cvdPlot(sub.med)ggarrange(sub.med,sub.med2,common.legend=TRUE,legend="right")#home comp
#nuts <- read.csv("/Volumes/Macintosh HD/Users/nicolakriefall/Google Drive (nicfall@bu.edu)/Moorea_revisions/env_revised/nuts_13-14_renamed.csv",header=T)
#work comp
nuts <- read.csv("~/nicfall@bu.edu - Google Drive/My Drive/Moorea_revisions/env_revised/nuts_13-14_renamed.csv",header=T)
str(nuts)## 'data.frame': 48 obs. of 11 variables:
## $ year : int 2013 2013 2013 2013 2013 2013 2013 2013 2013 2013 ...
## $ month : int 1 2 3 4 5 6 7 8 9 10 ...
## $ date : chr "1/20/13" "2/20/13" "3/20/13" "4/20/13" ...
## $ site : chr "Tiahura" "Tiahura" "Tiahura" "Tiahura" ...
## $ habitat : chr "Fore reef" "Fore reef" "Fore reef" "Fore reef" ...
## $ replicate : int 3 3 3 3 3 3 3 3 3 3 ...
## $ Phosphate_P2O5_uM: num 0.527 0.47 0.258 0.293 0.468 0.156 0.031 0.175 0.142 0.319 ...
## $ Nitrates_NO3_uM : num 0.108 0.101 0.114 0.164 0.023 0.186 0.039 0.049 0.009 0.011 ...
## $ Nitrites_NO2_uM : num 0.069 0.008 0.028 0.036 0.013 0.006 0.019 0.002 0.034 0.005 ...
## $ Silice_SiO2_uM : num 2.58 7.11 1.28 1.08 1.2 ...
## $ Ammonium_NH4_uM : num 4.637 2.198 1.06 0.473 0.55 ...
nuts$ym <- paste0(nuts$year,"_",nuts$month)
nuts$date2 <- as.Date(nuts$date,"%m/%d/%y")
str(nuts)## 'data.frame': 48 obs. of 13 variables:
## $ year : int 2013 2013 2013 2013 2013 2013 2013 2013 2013 2013 ...
## $ month : int 1 2 3 4 5 6 7 8 9 10 ...
## $ date : chr "1/20/13" "2/20/13" "3/20/13" "4/20/13" ...
## $ site : chr "Tiahura" "Tiahura" "Tiahura" "Tiahura" ...
## $ habitat : chr "Fore reef" "Fore reef" "Fore reef" "Fore reef" ...
## $ replicate : int 3 3 3 3 3 3 3 3 3 3 ...
## $ Phosphate_P2O5_uM: num 0.527 0.47 0.258 0.293 0.468 0.156 0.031 0.175 0.142 0.319 ...
## $ Nitrates_NO3_uM : num 0.108 0.101 0.114 0.164 0.023 0.186 0.039 0.049 0.009 0.011 ...
## $ Nitrites_NO2_uM : num 0.069 0.008 0.028 0.036 0.013 0.006 0.019 0.002 0.034 0.005 ...
## $ Silice_SiO2_uM : num 2.58 7.11 1.28 1.08 1.2 ...
## $ Ammonium_NH4_uM : num 4.637 2.198 1.06 0.473 0.55 ...
## $ ym : chr "2013_1" "2013_2" "2013_3" "2013_4" ...
## $ date2 : Date, format: "2013-01-20" "2013-02-20" ...
gg.new.pho <- ggplot(nuts,aes(x=date2,y=Phosphate_P2O5_uM,color=habitat,group=habitat,shape=habitat))+
geom_line()+
theme_cowplot()+
geom_point()+
geom_vline(xintercept=as.numeric(as.Date("2013-07-26")),linetype=4)+
geom_vline(xintercept=as.numeric(as.Date("2013-08-09")),linetype=4)+
scale_shape_manual(values=c(16,15))+
scale_colour_manual(values=c("#ED7953FF","#8405A7FF"),labels=c("Back reef","Fore reef"))+
#theme(legend.position="none")+
xlab("")+
ylab("Phosphates (µM)")+
labs(color="Habitat",shape="Habitat")
gg.new.phogg.new.nia <- ggplot(nuts,aes(x=date2,y=Nitrates_NO3_uM,color=habitat,group=habitat,shape=habitat))+
geom_line()+
theme_cowplot()+
geom_point()+
geom_vline(xintercept=as.numeric(as.Date("2013-07-26")),linetype=4)+
geom_vline(xintercept=as.numeric(as.Date("2013-08-09")),linetype=4)+
scale_shape_manual(values=c(16,15))+
scale_colour_manual(values=c("#ED7953FF","#8405A7FF"),labels=c("Back reef","Fore reef"))+
#theme(legend.position="none")+
xlab("")+
ylab("Nitrates (µM)")+
labs(color="Habitat",shape="Habitat")
gg.new.niagg.new.nii <- ggplot(nuts,aes(x=date2,y=Nitrites_NO2_uM,color=habitat,group=habitat,shape=habitat))+
geom_line()+
theme_cowplot()+
geom_point()+
geom_vline(xintercept=as.numeric(as.Date("2013-07-26")),linetype=4)+
geom_vline(xintercept=as.numeric(as.Date("2013-08-09")),linetype=4)+
scale_shape_manual(values=c(16,15))+
scale_colour_manual(values=c("#ED7953FF","#8405A7FF"),labels=c("Back reef","Fore reef"))+
#theme(legend.position="none")+
xlab("")+
ylab("Nitrites (µM)")+
labs(color="Habitat",shape="Habitat")
gg.new.niigg.new.sil <- ggplot(nuts,aes(x=date2,y=Silice_SiO2_uM,color=habitat,group=habitat,shape=habitat))+
geom_line()+
theme_cowplot()+
geom_point()+
geom_vline(xintercept=as.numeric(as.Date("2013-07-26")),linetype=4)+
geom_vline(xintercept=as.numeric(as.Date("2013-08-09")),linetype=4)+
scale_shape_manual(values=c(16,15))+
scale_colour_manual(values=c("#ED7953FF","#8405A7FF"),labels=c("Back reef","Fore reef"))+
#theme(legend.position="none")+
xlab("")+
ylab("Silica (µM)")+
labs(color="Habitat",shape="Habitat")
gg.new.silgg.new.amm <- ggplot(nuts,aes(x=date2,y=Ammonium_NH4_uM,color=habitat,group=habitat,shape=habitat))+
geom_line()+
theme_cowplot()+
geom_point()+
geom_vline(xintercept=as.numeric(as.Date("2013-07-26")),linetype=4)+
geom_vline(xintercept=as.numeric(as.Date("2013-08-09")),linetype=4)+
scale_shape_manual(values=c(16,15))+
scale_colour_manual(values=c("#ED7953FF","#8405A7FF"),labels=c("Back reef","Fore reef"))+
#theme(legend.position="none")+
xlab("")+
ylab("Ammonium (µM)")+
labs(color="Habitat",shape="Habitat")
gg.new.ammggarrange(gg.new.pho,gg.new.nia,gg.new.nii,gg.new.sil,gg.new.amm,labels="AUTO",common.legend=TRUE,legend="right",nrow=5)#ggsave("env_nutrients_revised.pdf",height=12)ggplot(nuts,aes(x=habitat,y=Phosphate_P2O5_uM))+
geom_boxplot()+
facet_wrap(~year)ggplot(nuts,aes(x=habitat,y=Nitrates_NO3_uM))+
geom_boxplot()+
facet_wrap(~year)ggplot(nuts,aes(x=habitat,y=Nitrites_NO2_uM))+
geom_boxplot()+
facet_wrap(~year)ggplot(nuts,aes(x=habitat,y=Silice_SiO2_uM))+
geom_boxplot()+
facet_wrap(~year)ggplot(nuts,aes(x=habitat,y=Ammonium_NH4_uM))+
geom_boxplot()+
facet_wrap(~year)gg.pho <- ggplot(nuts,aes(x=habitat,y=Phosphate_P2O5_uM,color=habitat,shape=habitat))+
geom_violin()+
#geom_jitter(alpha=0.7)+
theme_cowplot()+
geom_boxplot(width=0.1,alpha=0)+
scale_shape_manual(values=c(16,15),labels=c("BR","FR"))+
scale_x_discrete(labels=c("BR","FR"))+
scale_colour_manual(values=c("#ED7953FF","#8405A7FF"),labels=c("Back reef","Fore reef"))+
theme(legend.position="none")+
xlab("Habitat")+
ylab("Phosphates (µM)")
gg.pholibrary(car)## Loading required package: carData
##
## Attaching package: 'car'
## The following object is masked from 'package:dplyr':
##
## recode
nuts$habitat <- as.factor(nuts$habitat)
shapiro.test(log(nuts$Phosphate_P2O5_uM))##
## Shapiro-Wilk normality test
##
## data: log(nuts$Phosphate_P2O5_uM)
## W = 0.95694, p-value = 0.07596
leveneTest(nuts$Phosphate_P2O5_uM,nuts$habitat)#ns## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 1 0.0922 0.7627
## 46
summary(aov(Phosphate_P2O5_uM~habitat,data=nuts)) #ns## Df Sum Sq Mean Sq F value Pr(>F)
## habitat 1 0.0025 0.00251 0.049 0.826
## Residuals 46 2.3566 0.05123
#wilcox.test(Phosphate_P2O5_uM~habitat,data=nuts,exact=FALSE) #nsgg.nia <- ggplot(nuts,aes(x=habitat,y=Nitrates_NO3_uM,color=habitat,shape=habitat))+
geom_violin()+
#geom_jitter(alpha=0.7)+
geom_boxplot(width=0.1,alpha=0)+
theme_cowplot()+
scale_shape_manual(values=c(16,15),labels=c("BR","FR"))+
scale_x_discrete(labels=c("BR","FR"))+
scale_colour_manual(values=c("#ED7953FF","#8405A7FF"),labels=c("Back reef","Fore reef"))+
theme(legend.position="none")+
xlab("Habitat")+
ylab("Nitrates (µM)")
gg.niashapiro.test(log(nuts$Nitrates_NO3_uM)) #no##
## Shapiro-Wilk normality test
##
## data: log(nuts$Nitrates_NO3_uM)
## W = 0.91919, p-value = 0.002784
leveneTest(nuts$Nitrates_NO3_uM,nuts$habitat)#ns## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 1 2.3953 0.1286
## 46
#summary(aov(Nitrates_NO3_uM~habitat,data=nuts)) #p < 0.01**
wilcox.test(Nitrates_NO3_uM~habitat,data=nuts,exact=FALSE) #p < 0.01**##
## Wilcoxon rank sum test with continuity correction
##
## data: Nitrates_NO3_uM by habitat
## W = 435, p-value = 0.002519
## alternative hypothesis: true location shift is not equal to 0
# Wilcoxon rank sum test with continuity correction
#
# data: Nitrates_NO3_uM by habitat
# W = 435, p-value = 0.002519
sum.nia <- summarySE(data=nuts,measurevar="Nitrates_NO3_uM",groupvars="habitat")
sum.nia## habitat N Nitrates_NO3_uM sd se ci
## 1 Back reef 24 0.171250 0.08852278 0.01806964 0.03737989
## 2 Fore reef 24 0.094625 0.05985476 0.01221780 0.02527445
gg.nii <- ggplot(nuts,aes(x=habitat,y=Nitrites_NO2_uM,color=habitat,shape=habitat))+
geom_violin()+
#geom_jitter(alpha=0.7)+
geom_boxplot(width=0.1,alpha=0)+
theme_cowplot()+
scale_shape_manual(values=c(16,15),labels=c("BR","FR"))+
scale_x_discrete(labels=c("BR","FR"))+
scale_colour_manual(values=c("#ED7953FF","#8405A7FF"),labels=c("Back reef","Fore reef"))+
theme(legend.position="none")+
xlab("Habitat")+
ylab("Nitrites (µM)")
gg.niishapiro.test(nuts$Nitrites_NO2_uM)##
## Shapiro-Wilk normality test
##
## data: nuts$Nitrites_NO2_uM
## W = 0.94972, p-value = 0.03897
#summary(aov(Nitrites_NO2_uM~habitat,data=nuts)) #p < 0.05*
wilcox.test(Nitrites_NO2_uM~habitat,data=nuts,exact=FALSE) #p < 0.01**##
## Wilcoxon rank sum test with continuity correction
##
## data: Nitrites_NO2_uM by habitat
## W = 417, p-value = 0.008029
## alternative hypothesis: true location shift is not equal to 0
sum.nii <- summarySE(data=nuts,measurevar="Nitrites_NO2_uM",groupvars="habitat")
sum.nii## habitat N Nitrites_NO2_uM sd se ci
## 1 Back reef 24 0.03216667 0.01396476 0.002850544 0.005896801
## 2 Fore reef 24 0.02083333 0.01636185 0.003339849 0.006909003
gg.sil <- ggplot(nuts,aes(x=habitat,y=Silice_SiO2_uM,color=habitat,shape=habitat))+
geom_violin()+
#geom_jitter(alpha=0.5)+
geom_boxplot(width=0.1,alpha=0)+
theme_cowplot()+
scale_shape_manual(values=c(16,15),labels=c("BR","FR"))+
scale_x_discrete(labels=c("BR","FR"))+
scale_colour_manual(values=c("#ED7953FF","#8405A7FF"),labels=c("Back reef","Fore reef"))+
theme(legend.position="none")+
xlab("Habitat")+
ylab("Silica (µM)")
gg.silsummary(aov(Silice_SiO2_uM~habitat,data=nuts)) #ns## Df Sum Sq Mean Sq F value Pr(>F)
## habitat 1 0.19 0.1948 0.161 0.69
## Residuals 46 55.59 1.2084
wilcox.test(Silice_SiO2_uM~habitat,data=nuts) #ns##
## Wilcoxon rank sum exact test
##
## data: Silice_SiO2_uM by habitat
## W = 291, p-value = 0.9593
## alternative hypothesis: true location shift is not equal to 0
gg.amm <- ggplot(nuts,aes(x=habitat,y=Ammonium_NH4_uM,color=habitat,shape=habitat))+
geom_violin()+
#geom_jitter(alpha=0.5)+
geom_boxplot(width=0.1,alpha=0)+
theme_cowplot()+
scale_shape_manual(values=c(16,15),labels=c("BR","FR"))+
scale_x_discrete(labels=c("BR","FR"))+
scale_colour_manual(values=c("#ED7953FF","#8405A7FF"),labels=c("Back reef","Fore reef"))+
theme(legend.position="none")+
xlab("Habitat")+
ylab("Ammonium (µM)")
gg.ammsummary(aov(Ammonium_NH4_uM~habitat,data=nuts)) #ns## Df Sum Sq Mean Sq F value Pr(>F)
## habitat 1 0.00 0.0012 0.001 0.974
## Residuals 46 50.02 1.0873
wilcox.test(Ammonium_NH4_uM~habitat,data=nuts) #ns##
## Wilcoxon rank sum exact test
##
## data: Ammonium_NH4_uM by habitat
## W = 333, p-value = 0.3622
## alternative hypothesis: true location shift is not equal to 0
Results: - phosphates not sig, log-transformed anova - nitrates - nitrites - silica - ammonium
library(ggpubr)
ggarrange(gg.pho,gg.nia,gg.nii,gg.sil,gg.amm,labels="AUTO")#ggsave("env_nutrients.pdf",width=7)#home comp
#flowdat <- read.csv("/Volumes/Macintosh HD/Users/nicolakriefall/Google Drive (nicfall@bu.edu)/Moorea_revisions/env_revised/flow_rates_reformatted.csv",header=T)
#work comp
flowdat <- read.csv("~/nicfall@bu.edu - Google Drive/My Drive/Moorea_revisions/env_revised/flow_rates_reformatted.csv",header=T)
ggplot(flowdat,aes(x=site,y=speed_ms,fill=site))+
geom_boxplot()+
theme_cowplot()+
scale_shape_manual(values=c(16,15))+
scale_colour_manual(values=c("#ED7953FF","#8405A7FF"))+
scale_fill_manual(values=c("#ED7953FF","#8405A7FF"))+
ylab("Flow (m/s)")+
xlab("Site-reef zone")+
theme(legend.position="none")#ggsave("mnw.flow.pdf",width=2.5,height=2)
best.speed <- bestNormalize(flowdat$speed_ms)flowdat$speed.t <- best.speed$x.t
a.flow <- aov(speed.t~site,data=flowdat)
summary(a.flow)## Df Sum Sq Mean Sq F value Pr(>F)
## site 1 6128 6128 11195 <2e-16 ***
## Residuals 13536 7409 1
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(a.flow)## hat values (leverages) are all = 0.0001477323
## and there are no factor predictors; no plot no. 5
flow.sd <- summarySE(data=flowdat,measurevar="speed_ms",groupvars="site")
flow.sd## site N speed_ms sd se ci
## 1 MNW-B 6769 0.06481833 0.02387819 0.0002902279 0.0005689381
## 2 MNW-F 6769 0.10730170 0.02182916 0.0002653229 0.0005201163
sessionInfo()## R version 4.1.0 (2021-05-18)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Mojave 10.14.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] car_3.0-12 carData_3.0-4 ggpubr_0.4.0
## [4] Rmisc_1.5 plyr_1.8.6 lattice_0.20-45
## [7] bestNormalize_1.8.2 scales_1.1.1 colorBlindness_0.1.9
## [10] dplyr_1.0.7 cowplot_1.1.1 ggplot2_3.3.5
##
## loaded via a namespace (and not attached):
## [1] tidyr_1.1.4 splines_4.1.0 foreach_1.5.1 prodlim_2019.11.13
## [5] assertthat_0.2.1 highr_0.9 doRNG_1.8.2 yaml_2.2.1
## [9] globals_0.14.0 ipred_0.9-12 pillar_1.6.4 backports_1.3.0
## [13] glue_1.5.0 digest_0.6.28 ggsignif_0.6.3 colorspace_2.0-2
## [17] recipes_0.1.17 htmltools_0.5.2 Matrix_1.3-4 timeDate_3043.102
## [21] pkgconfig_2.0.3 broom_0.7.10 listenv_0.8.0 purrr_0.3.4
## [25] gower_0.2.2 lava_1.6.10 tibble_3.1.6 farver_2.1.0
## [29] generics_0.1.1 usethis_2.1.3 ellipsis_0.3.2 withr_2.4.2
## [33] nnet_7.3-16 survival_3.2-13 magrittr_2.0.1 crayon_1.4.2
## [37] evaluate_0.14 fs_1.5.0 fansi_0.5.0 future_1.23.0
## [41] parallelly_1.28.1 doParallel_1.0.16 MASS_7.3-54 rstatix_0.7.0
## [45] class_7.3-19 tools_4.1.0 lifecycle_1.0.1 stringr_1.4.0
## [49] munsell_0.5.0 rngtools_1.5.2 compiler_4.1.0 jquerylib_0.1.4
## [53] gridGraphics_0.5-1 rlang_0.4.12 grid_4.1.0 iterators_1.0.13
## [57] labeling_0.4.2 rmarkdown_2.11 gtable_0.3.0 codetools_0.2-18
## [61] abind_1.4-5 DBI_1.1.1 R6_2.5.1 gridExtra_2.3
## [65] lubridate_1.8.0 knitr_1.36 fastmap_1.1.0 future.apply_1.8.1
## [69] utf8_1.2.2 nortest_1.0-4 butcher_0.1.5 stringi_1.7.5
## [73] parallel_4.1.0 Rcpp_1.0.7 vctrs_0.3.8 rpart_4.1-15
## [77] tidyselect_1.1.1 xfun_0.28